Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007400.1 Hibiscus syriacus cultivar Beakdansim tig00019973_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65005
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:5293 original size:42 final size:42
Alignment explanation
Indices: 5234--5318 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
5224 GGGAAACGAA
*
5234 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
*
5276 CAGAGCTTTGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
5318 C
1 C
5319 GGCGAGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
Found at i:7907 original size:24 final size:24
Alignment explanation
Indices: 7850--7899 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
7840 AACAATAAAG
* *
7850 TATAAATATAAGTATATAATTATA
1 TATATATATAAGTATATAAGTATA
7874 TATATATATAAGTATATAAGTATA
1 TATATATATAAGTATATAAGTATA
7898 TA
1 TA
7900 AGTGTATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
TATATATATAAGTATATAAGTATA
Found at i:7908 original size:10 final size:8
Alignment explanation
Indices: 7855--7907 Score: 72
Period size: 8 Copynumber: 6.6 Consensus size: 8
7845 TAAAGTATAA
7855 ATATAAGT
1 ATATAAGT
*
7863 ATATAATT
1 ATATAAGT
7871 ATATATA-T
1 ATATA-AGT
7879 ATATAAGT
1 ATATAAGT
7887 ATATAAGT
1 ATATAAGT
7895 ATATAAGT
1 ATATAAGT
*
7903 GTATA
1 ATATA
7908 TGTTGAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 1 0.02
8 39 0.95
9 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (8 bp):
ATATAAGT
Found at i:8443 original size:50 final size:50
Alignment explanation
Indices: 8369--8481 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
8359 AATGTTTTTG
8369 CGAATAGTATTG-TACTGTATGAATAGTACCAATAATGTGTGAACAACAA
1 CGAATAGTATTGATACTGTATGAATAGTACCAATAATGTGTGAACAACAA
* * *** **
8418 CGAATAGTACTGATATTGTATGAATAGTATTGATAATGTGTGAACAGTAA
1 CGAATAGTATTGATACTGTATGAATAGTACCAATAATGTGTGAACAACAA
*
8468 CGAACAGTATTGAT
1 CGAATAGTATTGAT
8482 GCTCAAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 11 0.20
50 43 0.80
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (50 bp):
CGAATAGTATTGATACTGTATGAATAGTACCAATAATGTGTGAACAACAA
Found at i:8444 original size:20 final size:20
Alignment explanation
Indices: 8419--8466 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
8409 GAACAACAAC
*
8419 GAATAGTACTGATATTGTAT
1 GAATAGTACTGATAATGTAT
* *
8439 GAATAGTATTGATAATGTGT
1 GAATAGTACTGATAATGTAT
*
8459 GAACAGTA
1 GAATAGTA
8467 ACGAACAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (20 bp):
GAATAGTACTGATAATGTAT
Found at i:14839 original size:20 final size:20
Alignment explanation
Indices: 14814--14856 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
14804 TATATTGGGC
* *
14814 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
14834 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
14854 TAT
1 TAT
14857 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:17443 original size:15 final size:15
Alignment explanation
Indices: 17414--17457 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
17404 AAAAAATGGA
*
17414 AATAATTATAATATAT
1 AATAA-TATATTATAT
17430 GAAT-ATATATTATAT
1 -AATAATATATTATAT
17445 AATAATATATTAT
1 AATAATATATTAT
17458 GACACACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 18 0.72
16 1 0.04
17 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATAATATATTATAT
Found at i:17480 original size:2 final size:2
Alignment explanation
Indices: 17475--17747 Score: 73
Period size: 2 Copynumber: 141.5 Consensus size: 2
17465 ACACACACAC
17475 AT AT AT AT AT AT AT -T AT A- AT -T AT AT -T AT ACT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
17512 AT AT AT AT AT AA AGT AT -T A- AT AT -T GGT AT AT AA AGT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT -AT AT AT AT A-T AT AT
* **
17552 A- AA AT AT AT AGT AT A- AGT AT AT AT AT A- AT AT AT -T AT GC AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
17592 GT AT AT ACT -T A- AGT GT GT GT AT AT AT AT GT -T AT AC AT GT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
17633 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT GT GT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * * * * * *
17675 AT GT -T AT AC AT GT AT AT AT GT GT AT GT AT AT AT A- AA AGT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
17716 AT AT AT -T AT GT AT GT AC AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17748 CAAAAGTATA
Statistics
Matches: 200, Mismatches: 41, Indels: 60
0.66 0.14 0.20
Matches are distributed among these distances:
1 20 0.10
2 169 0.85
3 11 0.05
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (2 bp):
AT
Found at i:17520 original size:11 final size:11
Alignment explanation
Indices: 17478--17521 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
17468 CACACACATA
17478 TATATATATAT
1 TATATATATAT
17489 TATA-ATTATAT
1 TATATA-TATAT
17500 TATACT-TATAT
1 TATA-TATATAT
17511 TATATATATAT
1 TATATATATAT
17522 AAAGTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.07
11 27 0.93
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATATATAT
Found at i:17597 original size:37 final size:37
Alignment explanation
Indices: 17556--17747 Score: 130
Period size: 37 Copynumber: 5.2 Consensus size: 37
17546 GTATATAAAA
*
17556 TATATAGTATAAGTATATATATA-ATATATTATGCATG
1 TATATA-TATAAGTATATATATATATATATTATACATG
* * * *
17593 TATATACT-TAAGTGTGTGTATATATATGTTATACATG
1 TATATA-TATAAGTATATATATATATATATTATACATG
**
17630 TATATATAT-A-TATATATATATATATATTATATGTG
1 TATATATATAAGTATATATATATATATATTATACATG
* * * *
17665 TATATCATATATGT-TATACATGTATATATGTGT--ATG
1 TATAT-ATATAAGTATATATATATATATAT-TATACATG
* * * *
17701 TATATATAAAAGTACATATAT-TATGTATGTACATATATG
1 TATATATATAAGTATATATATATATATAT-T--ATACATG
17740 TATATATA
1 TATATATA
17748 CAAAAGTATA
Statistics
Matches: 121, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
35 38 0.31
36 29 0.24
37 40 0.33
38 3 0.02
39 11 0.09
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.46
Consensus pattern (37 bp):
TATATATATAAGTATATATATATATATATTATACATG
Found at i:17635 original size:57 final size:57
Alignment explanation
Indices: 17568--17708 Score: 169
Period size: 57 Copynumber: 2.4 Consensus size: 57
17558 TATAGTATAA
* *
17568 GTATATATATAATATATTATGCATGTATATACTTA-AGTGTGTGTAT-ATATATGTTATACAT
1 GTATATATAT-ATATA-TAT--ATATATATA-TTATA-TGTGTATATCATATATGTTATACAT
17629 GTATATATATATATATATATATATATATTATATGTGTATATCATATATGTTATACAT
1 GTATATATATATATATATATATATATATTATATGTGTATATCATATATGTTATACAT
* * *
17686 GTATATATGTGTATGTATATATA
1 GTATATATATATATATATATATA
17709 AAAGTACATA
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
56 11 0.15
57 44 0.60
59 3 0.04
60 5 0.07
61 10 0.14
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.48
Consensus pattern (57 bp):
GTATATATATATATATATATATATATATTATATGTGTATATCATATATGTTATACAT
Found at i:18518 original size:15 final size:15
Alignment explanation
Indices: 18498--18530 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
18488 AGTGTGATGA
18498 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
18513 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
18528 AAA
1 AAA
18531 AGAGCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (15 bp):
AAACCTATGGGGGAT
Found at i:18652 original size:13 final size:13
Alignment explanation
Indices: 18634--18658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18624 TAACATCACT
18634 TTTCTTTCATTTA
1 TTTCTTTCATTTA
18647 TTTCTTTCATTT
1 TTTCTTTCATTT
18659 TATGAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTCATTTA
Found at i:20329 original size:12 final size:12
Alignment explanation
Indices: 20312--20340 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20302 ACCTGAAAAG
20312 GTGAGTAACAGA
1 GTGAGTAACAGA
20324 GTGAGTAACAGA
1 GTGAGTAACAGA
20336 GTGAG
1 GTGAG
20341 CTTTGGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.38, T:0.17
Consensus pattern (12 bp):
GTGAGTAACAGA
Found at i:24703 original size:16 final size:15
Alignment explanation
Indices: 24682--24712 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
24672 ATTAAAAGAT
24682 ACATATATTTTTAAAA
1 ACATAT-TTTTTAAAA
24698 ACATATTTTTTAAAA
1 ACATATTTTTTAAAA
24713 TTCAAAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ACATATTTTTTAAAA
Found at i:24924 original size:24 final size:24
Alignment explanation
Indices: 24897--24942 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
24887 GATATTAGAA
* *
24897 ATCAAAAAATAATTCAGGTCAGAT
1 ATCAAAAAAGAATTCAGATCAGAT
* *
24921 ATCAGAACAGAATTCAGATCAG
1 ATCAAAAAAGAATTCAGATCAG
24943 GTACCGGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAAAAGAATTCAGATCAGAT
Found at i:26411 original size:13 final size:13
Alignment explanation
Indices: 26393--26425 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
26383 TAGGTACGAA
26393 TTCTCATGGTACT
1 TTCTCATGGTACT
26406 TTCTCATGGTACT
1 TTCTCATGGTACT
26419 TTCTCAT
1 TTCTCAT
26426 TAAGAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.48
Consensus pattern (13 bp):
TTCTCATGGTACT
Found at i:29332 original size:3 final size:3
Alignment explanation
Indices: 29324--29352 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29314 GATGATTGGG
29324 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
29353 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:29357 original size:3 final size:3
Alignment explanation
Indices: 29351--29389 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
29341 CAACAACAAC
29351 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29390 TGTGAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:32810 original size:32 final size:32
Alignment explanation
Indices: 32774--32850 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
32764 GTAGGCCCTG
*
32774 CGGCCCTAAGATGTGTTCTTAGGTAGGC-CTCA
1 CGGCCCTAAGATGT-ATCTTAGGTAGGCTCTCA
* * * *
32806 CGGCCCCAAAATCTATCTTGGGTAGGCTCTCA
1 CGGCCCTAAGATGTATCTTAGGTAGGCTCTCA
32838 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
32851 TCCCTTAGGT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
31 21 0.58
32 15 0.42
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Consensus pattern (32 bp):
CGGCCCTAAGATGTATCTTAGGTAGGCTCTCA
Found at i:37519 original size:42 final size:42
Alignment explanation
Indices: 37460--37544 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
37450 GGGAAACGAA
*
37460 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
*
37502 CAGAGCTTTGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
37544 C
1 C
37545 GGCGAGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
Found at i:39588 original size:9 final size:9
Alignment explanation
Indices: 39574--39633 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
39564 TATAATATAG
39574 TATAAAGTA
1 TATAAAGTA
*
39583 TATAAA-CA
1 TATAAAGTA
39591 -ATAAAGTA
1 TATAAAGTA
39599 TAAATATAAGTA
1 T--ATA-AAGTA
*
39611 TATAAATTA
1 TATAAAGTA
*
39620 TATAAACTA
1 TATAAAGTA
39629 TATAA
1 TATAA
39634 TATATGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
9 23 0.55
10 3 0.07
11 3 0.07
12 6 0.14
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (9 bp):
TATAAAGTA
Found at i:39593 original size:23 final size:22
Alignment explanation
Indices: 39552--39606 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
39542 ATGTATATAT
* * * *
39552 TATATATATATATATAATATAG
1 TATAAATATATAAACAATAAAG
39574 TATAAAGTATATAAACAATAAAG
1 TATAAA-TATATAAACAATAAAG
39597 TATAAATATA
1 TATAAATATA
39607 AGTATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (22 bp):
TATAAATATATAAACAATAAAG
Found at i:39643 original size:31 final size:31
Alignment explanation
Indices: 39552--39656 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 31
39542 ATGTATATAT
* *
39552 TATATATATATATAT-AA-TAT-AGTATAAAG
1 TATATAAATATATATAAACTATAAATAT-AAG
* *
39581 TATAT-AA-ACA-ATAAAGTATAAATATAAG
1 TATATAAATATATATAAACTATAAATATAAG
*
39609 TATATAAAT-TATATAAACTATATAATATATG
1 TATATAAATATATATAAACTATA-AATATAAG
*
39640 TATATAAGTATATATAA
1 TATATAAATATATATAA
39657 GTGTATATGT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.03
27 4 0.07
28 12 0.20
29 12 0.20
30 9 0.15
31 15 0.25
32 7 0.11
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (31 bp):
TATATAAATATATATAAACTATAAATATAAG
Found at i:39645 original size:39 final size:37
Alignment explanation
Indices: 39555--39663 Score: 112
Period size: 39 Copynumber: 2.8 Consensus size: 37
39545 TATATATTAT
*
39555 ATATATATATATAATATAGTATAAAGTATATAAACAATA
1 ATATATATATATAA-GTA-TATAAAGTATATAAACAATA
* *
39594 A-AGTATAAATATAAGTATATAAATTATATAAACTATATA
1 ATA-TATATATATAAGTATATAAAGTATATAAAC-A-ATA
* *
39633 ATATATGTATATAAGTATATATAAGTGTATA
1 ATATATATATATAAGTATATA-AAGTATATA
39664 TGTTGAACTA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
37 15 0.26
38 4 0.07
39 31 0.53
40 8 0.14
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (37 bp):
ATATATATATATAAGTATATAAAGTATATAAACAATA
Found at i:40546 original size:20 final size:20
Alignment explanation
Indices: 40521--40559 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40511 GTATTGGATG
40521 AATAGTACCGATACTATATA
1 AATAGTACCGATACTATATA
40541 AATAGTACCGATACTATAT
1 AATAGTACCGATACTATAT
40560 GAACAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (20 bp):
AATAGTACCGATACTATATA
Found at i:45511 original size:20 final size:20
Alignment explanation
Indices: 45486--45528 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
45476 TATATTGGGC
* *
45486 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
45506 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
45526 TAT
1 TAT
45529 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:45901 original size:13 final size:14
Alignment explanation
Indices: 45879--45907 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
45869 TTATAAATGT
45879 TTTTGTTAAACAAA
1 TTTTGTTAAACAAA
45893 TTTTG-TAAACAAA
1 TTTTGTTAAACAAA
45906 TT
1 TT
45908 ACTGTAGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTGTTAAACAAA
Found at i:48098 original size:8 final size:7
Alignment explanation
Indices: 48077--48119 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 7
48067 AAAAATGGAA
48077 ATAAT-T
1 ATAATAT
48083 ATAATAT
1 ATAATAT
48090 ATGAATAT
1 AT-AATAT
*
48098 ATATTAT
1 ATAATAT
48105 ATAATAAT
1 ATAAT-AT
48113 ATAATAT
1 ATAATAT
48120 GACACACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (7 bp):
ATAATAT
Found at i:48126 original size:2 final size:2
Alignment explanation
Indices: 48121--48169 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
48111 ATATAATATG
*
48121 AC AC AC AC AC AC AC AC AG AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
48163 AC AC AC A
1 AC AC AC A
48170 TATATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.47, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:48174 original size:2 final size:2
Alignment explanation
Indices: 48169--48235 Score: 95
Period size: 2 Copynumber: 34.5 Consensus size: 2
48159 ACACACACAC
*
48169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48211 AT -T AT ACT -T AT AT -T AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT A
48236 AAGTATTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
1 3 0.05
2 55 0.93
3 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:48274 original size:16 final size:16
Alignment explanation
Indices: 48252--48295 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
48242 TAATATTGGT
*
48252 ATATAAATTATATAAA
1 ATATAAAGTATATAAA
*
48268 CTATAAAGTATATAAA
1 ATATAAAGTATATAAA
*
48284 ATATATAGTATA
1 ATATAAAGTATA
48296 AGTATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (16 bp):
ATATAAAGTATATAAA
Found at i:48327 original size:37 final size:37
Alignment explanation
Indices: 48170--48368 Score: 76
Period size: 37 Copynumber: 5.3 Consensus size: 37
48160 CACACACACA
*
48170 TATATATATATA-TATATATATATATATATATATATATG
1 TATATATATA-AGTATATATATATATATAT-TATACATG
* *
48208 TATAT-TAT-ACT-TATAT-TATATATA-TATA-AAG
1 TATATATATAAGTATATATATATATATATTATACATG
** * * * *
48239 TAT-TAATATTGGTATATAAATTATATAAACTATA-AAG
1 TATAT-ATATAAGTATATATA-TATATATATTATACATG
*
48276 TATATAAAATATATAGTATAAGTATATATATAATATATTATGCATG
1 TATAT---ATATA-AG--T-A-TATATATAT-ATATATTATACATG
* * * *
48322 TATATACT-TAAGTGTGTGTATATATATGTTATACATG
1 TATATA-TATAAGTATATATATATATATATTATACATG
48359 TATATATATA
1 TATATATATA
48369 TATATTATAA
Statistics
Matches: 124, Mismatches: 17, Indels: 41
0.68 0.09 0.23
Matches are distributed among these distances:
30 1 0.01
31 5 0.04
32 7 0.06
33 1 0.01
34 12 0.10
35 6 0.05
36 9 0.07
37 33 0.27
38 13 0.10
40 6 0.05
41 1 0.01
42 2 0.02
43 4 0.03
44 5 0.04
45 12 0.10
46 7 0.06
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (37 bp):
TATATATATAAGTATATATATATATATATTATACATG
Found at i:48364 original size:17 final size:16
Alignment explanation
Indices: 48342--48412 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 16
48332 AGTGTGTGTA
48342 TATATATGTTATACAT
1 TATATATGTTATACAT
* *
48358 GTATATAT-ATATATAT
1 -TATATATGTTATACAT
48374 TATA-A-GTGTAT--AT
1 TATATATGT-TATACAT
*
48387 CATATATGTTATACAT
1 TATATATGTTATACAT
48403 GTATATATGT
1 -TATATATGT
48413 GTATGTGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
13 5 0.12
14 5 0.12
15 9 0.21
16 8 0.19
17 15 0.36
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (16 bp):
TATATATGTTATACAT
Found at i:48415 original size:10 final size:10
Alignment explanation
Indices: 48338--48464 Score: 62
Period size: 10 Copynumber: 12.0 Consensus size: 10
48328 CTTAAGTGTG
48338 TGTATATATA
1 TGTATATATA
*
48348 TGT-TATACA
1 TGTATATATA
48357 TGTATATATA
1 TGTATATATA
*
48367 TATATATTATAA
1 TGTATA-TAT-A
48379 GTGTATATCATATA
1 -TG--TAT-ATATA
*
48393 TGT-TATACA
1 TGTATATATA
*
48402 TGTATATATG
1 TGTATATATA
*
48412 TGTATGTGTATA
1 TGTA--TATATA
* *
48424 TATAAGTACATA
1 TGT-A-TATATA
*
48436 TGT-TATGTA
1 TGTATATATA
*
48445 TGTACATATA
1 TGTATATATA
48455 TGTATATATA
1 TGTATATATA
48465 CAAAAGTATA
Statistics
Matches: 87, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
9 22 0.25
10 35 0.40
11 4 0.05
12 14 0.16
13 4 0.05
14 1 0.01
15 6 0.07
16 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (10 bp):
TGTATATATA
Found at i:49241 original size:15 final size:15
Alignment explanation
Indices: 49221--49253 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
49211 AGTGTGACGA
49221 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
49236 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
49251 AAA
1 AAA
49254 AGAGCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (15 bp):
AAACCTATGGGGGAT
Found at i:49382 original size:12 final size:13
Alignment explanation
Indices: 49355--49382 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49345 TATAACATCA
49355 TTTTTCTTTCATT
1 TTTTTCTTTCATT
49368 TTTTTCTTTCATT
1 TTTTTCTTTCATT
49381 TT
1 TT
49383 ATGAATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTCATT
Found at i:51051 original size:12 final size:12
Alignment explanation
Indices: 51034--51086 Score: 88
Period size: 12 Copynumber: 4.4 Consensus size: 12
51024 ACCTGAAAAG
51034 GTGAGTAACAGA
1 GTGAGTAACAGA
*
51046 GTGAGTAACAAA
1 GTGAGTAACAGA
*
51058 GTGAGTAATAGA
1 GTGAGTAACAGA
51070 GTGAGTAACAGA
1 GTGAGTAACAGA
51082 GTGAG
1 GTGAG
51087 CTTTGGGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.34, T:0.19
Consensus pattern (12 bp):
GTGAGTAACAGA
Found at i:55450 original size:16 final size:15
Alignment explanation
Indices: 55429--55459 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
55419 ATTAAAAGAT
55429 ACATATATTTTTAAAA
1 ACATAT-TTTTTAAAA
55445 ACATATTTTTTAAAA
1 ACATATTTTTTAAAA
55460 TTAAAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ACATATTTTTTAAAA
Found at i:55670 original size:24 final size:24
Alignment explanation
Indices: 55643--55688 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
55633 GATATTAGAA
* *
55643 ATCAAAAAATAATTCAGGTCAGAT
1 ATCAAAAAAGAATTCAGATCAGAT
* *
55667 ATCAGAACAGAATTCAGATCAG
1 ATCAAAAAAGAATTCAGATCAG
55689 GTACCGGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAAAAGAATTCAGATCAGAT
Found at i:56067 original size:13 final size:13
Alignment explanation
Indices: 56049--56081 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
56039 TAGGTACGAA
56049 TTCTCATGGTACT
1 TTCTCATGGTACT
56062 TTCTCATGGTACT
1 TTCTCATGGTACT
56075 TTCTCAT
1 TTCTCAT
56082 TAAGAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.48
Consensus pattern (13 bp):
TTCTCATGGTACT
Found at i:57917 original size:3 final size:3
Alignment explanation
Indices: 57911--57937 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
57901 CAACAACAAC
57911 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
57938 TGTGAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:61934 original size:32 final size:31
Alignment explanation
Indices: 61860--61935 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
61850 CTAATGTGAC
* * *
61860 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** **
61891 TCTCGGGTAGGCCCTACGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
61923 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
61936 TCACAGCCCC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Done.